One of the most tedious recurring questions in the public debate about faith has been "is religion compatible with science?" Why won't it just go away?

I'm convinced that one reason is that the standard affirmative answer is sophisticated enough to persuade those willing to be persuaded, but fishy enough for those less sure to keep sniffing away at it. That defence is that religion and science are compatible because they are not talking about the same things. Religion does not make empirical claims about how the universe works, and to treat it as though it did is to make a category mistake of the worst kind. So we should just leave science and religion to get on with their different jobs free from mutual molestation.

The biologist Stephen Jay Gould made just this kind of move when he argued that science and religion have non-overlapping magisteria (noma). In Rock of Ages, Gould wrote that science deals with "the empirical realm: what the universe is made of (fact) and why does it work in this way (theory). The magisterium of religion extends over questions of ultimate meaning and moral value. These two magisteria do not overlap, nor do they encompass all inquiry." In short, science is empirical, religion is ethical.

A version of this strategy was also adopted by the physicist John Polkinghorne and the mathematician Nicholas Beale in their book, Questions of Truth. As they put it: "Science is concerned with the question, How? – By what process do things happen? Theology is concerned with the question, Why? – Is there a meaning and purpose behind what is happening?"

It sounds like a clear enough distinction, but maintaining it proves to be very difficult indeed. Many "why" questions are really "how" questions in disguise. For instance, if you ask: "Why does water boil at 100C?" what you are really asking is: "What are the processes that explain it has this boiling point?" – which is a question of how.

Critically, however, scientific "why" questions do not imply any agency – deliberate action – and hence no intention. We can ask why the dinosaurs died out, why smoking causes cancer and so on without implying any intentions. In the theistic context, however, "why" is usually what I call "agency-why": it's an explanation involving causation with intention.

So not only do the hows and whys get mixed up, religion can end up smuggling in a non-scientific agency-why where it doesn't belong.

This means that if someone asks why things are as they are, what their meaning and purpose is, and puts God in the answer, they are almost inevitably going to make an at least implicit claim about the how: God has set things up in some way, or intervened in some way, to make sure that purpose is achieved or meaning realised. The neat division between scientific "how" and religious "why" questions therefore turns out to be unsustainable.

Consider, for example, anthropic fine-tuning, which the religious physicist, Paul Davies, calls "The Goldilocks Enigma": the conditions in the universe are just right for life to have evolved, and had a few things been just slightly different at the Big Bang, none of us would be here. At the moment, there is no generally accepted scientific explanation for why or how this is so. Taking off his physicist's coat and donning his theologian's hat, Polkinghorne answers the "why" question by saying that the life-enabling laws of physics are "graciously provided by the creator". Not only does this introduce agency-why where we'd normally just look for scientific-why, it is also a claim about how the universe came to be this way, namely, by divine fiat. It trespasses onto the "how" territory of science, but since it cannot explain the mechanism by which God intervened, nor test the hypothesis that he did so, it is no substitute for a proper scientific answer.

Of course, there are ways of understanding religion that do not fall into this trap. A Spinozistic "God-or-nature" could act with a purpose that was, at root, simply the playing out of natural forces. But the theistic God is "behind" what happens, not simply part of it.

Alternatively, you might say – indeed many do – that religion is not about belief at all, and so never explains anything in terms of agency-why. I'll be saying more about this approach in future posts. But for the moment, we can say that any religious belief that involves an activist, really-existing God and claims that religion has something to say about why things happen, must also be encroaching on questions of how they happen, too. And if that's true, the easy peace which many claim should exist between science and religion just isn't possible.

The religious believer could bite the bullet, accept that religion does make some empirical claims, and then defend their compatibility with science one by one. But the fact that two beliefs are compatible with each other is the most minimal test of their reasonableness imaginable. All sorts of outlandish beliefs – that the Apollo moon landings never happened, for instance – are compatible with science, but that hardly makes them credible. What really counts, what should really make the difference between assent and rejection of an empirical claim, is not whether it is compatible with science, but whether an evidence-led, rational examination of a view supports it better than competing alternatives.

So the fact that science is compatible with religion turns out to be a comforting red herring.

The less comfortable wet fish slapped around the face is that how easily science and religion can rub on together depends very much on what kind of religion we're talking about. If it is a kind that seeks to explain the hows of the universe, or ends up doing so by stealth, then it is competing with science. In such contests science always wins, hands down, and the only way out is to claim a priority for faith over evidence, or the Bible over the lab. If it is of a kind that doesn't attempt to explain the hows of the universe, then it has to be very careful not to make any claims that end up doing just that. Only then can the science v religion debate move on, free from the illusion that it rests on one question with one answer.